[pagoda] Move project to Scala

This commit includes a few changes:
- The repository still uses Maven to manage dependency but it is now a
  Scala project.
- The code has been ported from OWLAPI 3.4.10 to 5.1.20
- A proof of concept program using both RSAComb and PAGOdA has been
  added.

1 files changed, 0 insertions, 79 deletions

diff --git a/test/resources/answers/pagoda-fly-with-GJ-FC-individuals.json b/test/resources/answers/pagoda-fly-with-GJ-FC-individuals.json
deleted file mode 100644
index e37d3f5..0000000
--- a/test/resources/answers/pagoda-fly-with-GJ-FC-individuals.json
+++ /dev/null
@@ -1,79 +0,0 @@
-[
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT distinct ?X WHERE { ?X rdf:type obo:FBbt_00005106 . ?X obo:RO_0002131 ?Y . ?Y rdf:type obo:FBbt_00007401 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 1,
-    "answers": []
-  },
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> PREFIX FBbt: <http://purl.obolibrary.org/obo/FBbt#> SELECT distinct ?X WHERE { ?X rdf:type obo:FBbt_00005106 . ?X obo:RO_0002131 ?Y . ?Y rdf:type obo:FBbt_00007401 . ?X FBbt:develops_from ?Z . ?Z rdf:type obo:FBbt_00067346 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 2,
-    "answers": []
-  },
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT distinct ?X WHERE { ?X rdf:type obo:FBbt_00100388 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 3,
-    "answers": [
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100696>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100030>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100700>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100566>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100314>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100332>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100436>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100443>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100051>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100372>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100480>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100462>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100195>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100103>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100251>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100225>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100527>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100164>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100008>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100722>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100383>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100186>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100177>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100206>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100446>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100224>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100706>",
-      "<http://www.virtualflybrain.org/ontologies/individuals/VFB_00100360>"
-    ]
-  },
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT distinct ?X WHERE { ?X rdf:type obo:FBbt_00007173 . ?X obo:RO_0002131 ?Y . ?Y rdf:type obo:FBbt_00003924 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 4,
-    "answers": []
-  },
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT distinct ?X WHERE { ?X obo:RO_0002131 ?Y . ?Y rdf:type obo:FBbt_00005801 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 5,
-    "answers": []
-  },
-  {
-    "queryText": "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> PREFIX obo: <http://purl.obolibrary.org/obo/> SELECT distinct ?X WHERE { ?X obo:RO_0002130 ?Y . ?Y rdf:type obo:FBbt_00007053 }",
-    "answerVariables": [
-      "X"
-    ],
-    "queryID": 6,
-    "answers": []
-  }
-]
\ No newline at end of file